Although inflammatory mechanisms are clearly associated with organic gastrointestinal (GI) disorders, such as the Inflammatory Bowel Disease, the involvement of inflammation with functional gastrointestinal disorders and chronic GI symptoms such as diarrhea and chronic abdominal pain (CAP) with no identified organic cause is unclear. We found evidence for differential levels of specific candidate biomarkers in GI biopsies from patients with histologically defined inflammatory phenotypes in the absence of organic GI disorders. The IL-6 levels in the colonic biopsies from pediatric patients with inflammatory phenotypes were found to be significantly increased compared to controls with non-inflammatory phenotypes (Henderson, et al., 2012, WJGP). In the same colonic biopsies, the number of mast cells was significantly higher in patients with no evidence of histological inflammation compared to patients with inflammatory phenotype. Interestingly, no difference in IL-6 and mast cell staining was observed in the upper GI tract biopsies, suggesting significance of the colonic environment in chronic GI symptom pathology. Such significance was corroborated by our results using an intestinal permeability test solution, ingested by participants following an overnight fast. The test solution contains four sugar probes absorbable at various sites along the GI tract. Five hours after ingestion, excreted urine analysis of the four sugar probes and raffinose (an internal standard) was performed using mass spectrometry method. Based on these analyses, we showed that patients with CAP, meeting Rome III criteria for Irritable Bowel Syndrome (IBS), had a significantly decreased colonic permeability, represented by differential urinary sucralose output, compared to controls with no IBS. Of the IBS patients, 55% had diarrhea. Changes in sucrose urine output, representing gastric permeability, and changes in lactulose-to-mannitol ratio, representing small intestinal permeability, were not observed (Del Valle-Pinero, et al., 2013). This unexpected finding, which points to altered colonic permeability as one of the likely mechanisms for the observed GI aberrations in patient with chronic GI symptoms, together with our histological evidence from the colonic biopsies, serve as a starting point for a closer investigation into candidate cellular and molecular players within the pathways and microenvironment contributing to chronic GI symptoms. Our preliminary investigation of such molecular players recently revealed mRNA and microRNA (miR) signatures associated with carefully phenotyped patients having chronic GI symptoms. In IBS patients, we found elevated levels of two circulating miRs, the hsa-miR-342-3p and hsa-miR-150, compared to controls with similar age, BMI, and ethnicity (Fourie, et al., 2014). Within the IBS group, IBS-constipation patients but not the IBS-diarrhea patients had elevated hsa-miR-342-3p level compared to controls. The involvement of inflammation is suggested by these specific miRs, which are linked to inflammation in other diseases, e.g., cancer. Other miR signatures were further found in a subset of patients with Non-alcoholic Fatty Liver Disease (NAFLD). Male NAFLD patients had significantly upregulated expressions of the hsa-miR-432-5p, hsa-miR-578 and hsa-miR-155-5p compared to female NAFLD patients. Because some of these miRs are known to play a role in inflammatory mechanisms, this finding suggests a gender-specific inflammatory miR signature in NAFLD. Further, we found that male NAFLD patients had higher hsa-miR-432-5p levels compared to male controls, whereas no miRs were found to be differential in their levels between female NAFLD patients and female controls. Thus, this pilot study showed empirical evidence for a male-specific miR profile in NAFLD (Longchamps, et al., 2014). In addition to these miRs, we found candidate mRNA biomarkers which have been associated with inflammation: chemokine C-C motif ligand 16 (CCL-16) and the Vasoactive Intestinal Peptide (VIP), in IBS patients compared to controls. Within subsets of IBS patients, the CCL-16 gene expression was also upregulated in IBS patients having chronic constipation, compared to both controls and IBS patients having chronic diarrhea (Del Valle Pinero, et al., 2011). In light of the recent finding by others elucidating enhancement of CCL-16 protein function as a haptotactic gradient regulator for two key inflammatory cells, the monocytes and the lymphocytes, by matrix metalloproteases, our finding provides further evidence for a subclinical inflammatory mechanism in these patients. Likewise, the VIP gene expression from peripheral whole blood was significantly upregulated by 2.91-fold in IBS patients when compared to controls (Del Valle Pinero, et al., 2015). VIP is currently being looked at as a possible drug or therapeutic target for a number of GI disorders, because it is released in response to inflammation in the GI tract and suppresses the immune system causing a reduction in the inflammation. To further evaluate findings of circulating miRs and mRNAs in patients with chronic GI dysfunction as a host organism, we identified epithelial mucosa-adherent microbiome signatures in patients with IBS compared to controls (Fourie, et al., 2016). In an exploratory study, we examined whether differences exist in the oral microbiome of IBS participants compared to healthy controls, and whether the oral microbiome relates to symptom severity. The oral buccal mucosal microbiome of 38 participants was characterized using PhyloChip microarrays. Participants self-reported the severity of induced abdominal pain following ingestion of the previously utilized (Del Valle-Pinero, et al., 2013) four-sugar probe intestinal permeability test solution. Induced abdominal pain post-ingestion was most severe in IBS participants (P = 0.0002), particularly those who were overweight (P = 0.02), and was robustly correlated to the abundance of 60 OTUs, 4 genera, 5 families and 4 orders of bacteria (r2 > 0.4, P < 0.001). IBS-overweight participants showed decreased richness in the phylum Bacteroidetes (P = 0.007) and the genus Bacillus (P = 0.008) and a significant separation of the IBS-overweight group (P < 0.05) was evident through analysis of beta-diversity. Our oral microbial results are concordant with described fecal and colonic microbiome-IBS and -weight associations. Having IBS and being overweight, rather than IBS-subtypes (chronic constipation or diarrhea), was the most important factor in describing the severity of induced abdominal pain and variation in the microbiome. Further, pain severity was strongly correlated to taxa-specific abundance, suggesting oral microbiomes potential utilization in diagnosis and clinical phenotyping. We are currently examining these microbiome results in conjunction with the circulating molecular signatures in order to elucidate mechanisms underlying the observed altered colonic permeability in patients with chronic GI dysfunction. We utilize cell and animal models to investigate implications on gut epithelial barrier dynamics. Also, due to the increasingly recognized link between gut epithelial barrier dynamics and neurological function (Brain-Gut interactions), we examine the genetics of neuro-related behaviors, such as chronic stress and sleep, in our patients (Heitkemper, et al., 2015 and Reddy, et al., 2014). Laboratory experiments designed to further explore these dynamics are in progress.